The largest database of trusted experimental protocols

Dataanalysis version 5

Manufactured by Bruker

DataAnalysis Version 5.0 is a software application developed by Bruker for data analysis and visualization. The software is designed to handle and process data from various Bruker instruments and equipment. It provides users with tools for data management, analysis, and presentation.

Automatically generated - may contain errors

6 protocols using dataanalysis version 5

1

Quantification of SHP2 Inhibitor Binding

Check if the same lab product or an alternative is used in the 5 most similar protocols
Samples were prepared essentially as described for the reversibility assay, except samples of 100 μM SHP2 with 120 μM 99 or vehicle-only (DMSO) were incubated in PTP buffer 1 (see above) supplemented with 1 mM DTT at 4% v/v DMSO before washing. After washing, LC-MS analysis was performed at the University of Massachusetts Amherst Mass Spectrometry Core Facility. Protein samples were diluted 1:1 with 0.2% formic acid and 10 μg of protein was injected onto an Acquity Protein BEH C4, 300 Å, 1.7 mm, 2.1 × 50 mm column (Waters, Milford, MA) connected to an Agilent 1100 HPLC system. The mobile phases were (A) 0.1% formic acid and (B) 0.1% formic acid in 99% acetonitrile. The system was equilibrated in 30% B at a flow rate of 150 μL/min and the following gradient was applied following sample injection: 30% B for 1 min, 30–75% B over 5 min, 75–90% B over 1 min, 90% B for 2 min. The flow was infused into a 7 T solariX FTICR mass spectrometer (Bruker, Billerica, MA) equipped with a standard electrospray source. The capillary voltage was 4.5 kV, dry gas flow of 8 L/min and dry gas temperature of 200 °C. MS spectra were acquired over 300 – 3,000 m/z with a 128 K transient size and 0.2 sec accumulation time. Data was processed using DataAnalysis Version 5.0 (Bruker).
+ Open protocol
+ Expand
2

SapB:Gb3-NBD Crystal Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Several dozen SapB:Gb3-NBD crystals were individually looped and twice-washed in 3.4 M malonate pH 5 buffer and dissolved in Mili-Q water, yielding a final absorbance of 0.03 at 280nm (~ 0.82 mg/mL). Samples were diluted to 0.1 mg/mL with 0.1% formic acid, and 10 μl was injected onto a Grace Vydac 214TP C4, 2.1 × 50 mm column (Hichrom, Leicestershire, UK) connected to an Agilent 1100 HPLC system with a binary pump. The mobile phases were (A) 0.1% formic acid and (B) 0.1% formic acid in 99% acetonitrile. The system was equilibrated in 10% B at a flow rate of 250 μL/min and the following gradient was applied: 10% B for 1 min, 10–60% B over 5 min, 60–90% B over 2 min, 90% B for 1min. The flow was infused into a 7 T solariX FTICR mass spectrometer (Bruker, Billerica, MA) equipped with a standard electrospray source. The capillary voltage was 4.5 kV, dry gas flow of 8 L/min and dry gas temperature of 200 °C. MS spectra were acquired over 200 – 3,000 m/z with a 256 Kword transient size and 0.2 sec accumulation time. Data were processed using DataAnalysis Version 5.0 (Bruker).
+ Open protocol
+ Expand
3

Tryptic Digestion and LC-MS/MS Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Following tryptic digestion, samples were separated and analyzed with an Ultimate 3000 Nano HPLC system (Thermo Scientific) interfaced to a Bruker Maxis quadrupole time-of-flight MS instrument. Detailed information on these analyses can be found in the ESM Section S1.2. Identification of proteins was performed with the search engine Mascot (version 2.301). Raw MS data were converted into centroided peak lists using DataAnalysis version 5.0 (Bruker). The parameters used for Mascot searches were set as follows: enzyme specificity, semiTrypsin; missed cleavages, 2; fixed modification, carbamidomethyl (C); variable modification, oxidation (M) peptide mass tolerance, 0.1%; fragment mass tolerance, 0.05 Da; no restriction for species was used. The instrument was set to ESI-QUAD-TOF.
+ Open protocol
+ Expand
4

SHP2 Inhibitor 99 Analysis by LC-MS

Check if the same lab product or an alternative is used in the 5 most similar protocols
Samples were prepared essentially as described for
the reversibility assay, except samples of 100 μM SHP2 with
120 μM 99 or vehicle-only (DMSO) were incubated
in PTP buffer 1 (see above) supplemented with 1 mM DTT at 4% (v/v)
DMSO before washing. After washing, LC-MS analysis was performed at
the University of Massachusetts Amherst Mass Spectrometry Core Facility.
Protein samples were diluted in a 1:1 ratio with 0.2% formic acid,
and 10 μg of protein was injected onto an Acquity Protein BEH
C4 column (300 Å, 1.7 mm, 2.1 mm × 50 mm; Waters, Milford,
MA) connected to an Agilent 1100 HPLC system. The mobile phases were
(A) 0.1% formic acid and (B) 0.1% formic acid in 99% acetonitrile.
The system was equilibrated in 30% B at a flow rate of 150 μL/min,
and the following gradient was applied following sample injection:
30% B for 1 min, 30% to 75% B over 5 min, 75% to 90% B over 1 min,
and 90% B for 2 min. The flow was infused into a 7 T solariX FTICR
mass spectrometer (Bruker, Billerica, MA) equipped with a standard
electrospray source. The capillary voltage was 4.5 kV, the dry gas
flow 8 L/min, and the dry gas temperature 200 °C. MS spectra
were acquired over the range of m/z 300–3000 with a 128 K transient size and a 0.2 s accumulation
time. Data were processed using DataAnalysis version 5.0 (Bruker).
+ Open protocol
+ Expand
5

ESI-QTOF-MS Metabolomics Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols
LC-MS analyses were performed with an ESI-QTOF-MS system (Impact II, Bruker, Billerica, MA, USA) coupled with a liquid chromatography system (1290 Infinity, Agilent) and equipped with a reversed-phase Agilent Zorbax SB-C18 column (2.1 mm × 50 mm, 1.8 µm). Mobile phases were water with 0.1% formic acid (A) and acetonitrile with 0.1% formic acid (B). The following gradient elution method was used: 0 to 95% B from 0 to 45 min, a 95% B plateau for 10 min, and a return to initial conditions with equilibration for 10 min. The column temperature was set at 40 °C, and the flow rate was 0.25 mL/min. The samples were kept in an autosampler at 10 °C. Each sample was injected at a volume of 10 μL. The operating parameters of the mass spectrometer were as follows: negative spray voltage at 3500 V, dry temperature at 200 °C, dry gas flow at 8 L/min, and nebulizer at 1 bar. The data were collected with a mass range from 50 to 2500 m/z with an acquisition rate of 8 Hz and stepping. The Auto MS/MS mode was used to obtain fragment ions. The instrument was calibrated using a Tune mix standard solution before the runs, and, at the beginning of each run, this solution was injected as an internal calibrant for MS spectrum calibration. The LC-MS-acquired data were processed using DataAnalysis Version 5.2 software (Bruker) and Metaboscape Version 2023b software (Bruker).
+ Open protocol
+ Expand
6

LC-MS Analysis of Chemical Compounds

Check if the same lab product or an alternative is used in the 5 most similar protocols
LC-MS analyses were performed with an ESI-QTOF-MS system (Impact II, Bruker, Billerica, MA, USA) coupled with a liquid chromatography system (1290 Infinity, Agilent) and equipped with a reversed-phase InertSustain AQ-C18 column (100 × 2.1 mm; 3 µm) GL Sciences Inc. Mobile phases were water with 0.1% formic acid (A) and acetonitrile with 0.1% formic acid (B). The following gradient elution method was used: 5% B from 0 to 1 min, 5−60% B from 1 to 12 min, a 60% B plateau for 12 to 16 min, 60−80% B from 16 to 20 min, an 80% B plateau for 3 min and a return to initial conditions with equilibration for 6 min. The column temperature was set at 30 °C, and the flow rate was 0.4 mL/min. The samples were kept in an autosampler at 4 °C. Each sample was injected at a volume of 10 μL. The operating parameters of the mass spectrometer were as follows: positive spray voltage at 4000 V, dry temperature at 250 °C, dry gas flow at 10 L/min and nebulizer at 3 bar. The data were collected with a mass range from 50 to 1000 m/z. The instrument was calibrated using a 10 mM sodium formate solution before the runs, and, at the beginning of each run, this solution was injected as an internal calibrant for MS spectrum calibration. The LC-MS acquired data were processed using DataAnalysis Version 5.2 software (Bruker) to extract the mass spectra from the sample raw data.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!